The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints

Danny S. Tuckwell, Matthew J. Nicholson, Christopher S. McSweeney, Michael K. Theodorou and Jayne L. Brookman (2005). The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints. Microbiology, 151 (5) pp.1557-1567 Sponsorship: BBSRC / Stapledon Memorial Trust RAE2008

Project Sanitarium: gaming TB: a serious game for a serious problem

Collaborative projects between Industry and Academia provide excellent opportunities for learning. Throughout the academic year 2014-2015 undergraduates from the School of Arts, Media and Computer Games at Abertay University worked with academics from the Infection Group at the University of St Andrews and industry partners Microsoft and DeltaDNA. The result was a serious game prototype that utilized game design techniques and technology to demystify and educate players about the diagnosis and treatment of one of the world's oldest and deadliest diseases, Tuberculosis (TB). Project Sanitarium is a game incorporating a mathematical model that is based on data from real-world drug trials. This paper discusses the project design and development, demonstrating how the project builds on the successful collaborative pedagogical model developed by academic staff at Abertay University. The aim of the model is to provide undergraduates with workplace simulation, wider industry collaboration and access to academic expertise to solve challenging and complex problems.

The Offstage of Democracy: The Problem of Social Dialogue in John Dewey’s and Walter Lippmann’s Writings

The aim of this article is to present and discuss John Dewey’s and Walter Lippmann’s views on the problem of communication in a democratic society, particularly their views on the question of a role of communication in forming social processes. First part of the paper outlines the framework of this problem and its meaning to the question of possibility of democracy. Part two is concerned with anthropological and socio-political considerations: I discuss the Deweyan and the Lippmannian understanding of individual, society, intelligence and democracy. In part three I examine in detail the problem of communication, with special attention given to the questions of the role of communication in forming social processes, the foundations and conditions of communication, the debaters, and a subject matter of a debate as well as the questions of who and what forms this debate and whether we can form it altogether.

Problem ubóstwa w Unii Europejskiej

The issues of poverty, famine and malnutrition mainly concern underdeveloped regions. Yet in recent years the proportion of the population threatened with poverty and social exclu- sion has been growing not only in these regions but also in developed areas, including the EU. The issue of poverty is additionally related to demography. In this context, the aging popula- tion of West European countries is worrisome, as the elderly are one of the groups particularly threatened by poverty, and their number continues to grow. Appreciating the gravity of this is- sue, the European Commission considers the fight against poverty to be one of the basic five directions established in the Europe 2020 strategic document.

Sytuacja społeczna ludzi starych jako problem pedagogiczny

In the article were presented results and analysis of searches of social situation of older people. A general purpose of searches was to qualify outer impulses which are components of aspect of social situation and that how it is accepted by older people and how it stimulates their activity. Learning of social situation of older people allows to qualify specific methods of work with them on base of pedagogics.

Refugee Question as an International Global Problem

The problem of refugees is a phenomenon characteristic of contemporary international relations. It can take an individual form (as a result of individual persecutions of a racial, religious, national or political character) or the form of mass relocations, especially in the face of military conflicts or general breaching of human rights. The purpose of this paper is to present the refugee question as an international global problem that may appear in any region of the world, impacting the situation of states and societies, that is perceived as both a threat and a fundamental challenge for the entire international community.

Konwencja dotycząca statusu uchodźców a praktyka turecka. Problem przybyszów zza wschodniej granicy

Celem publikacji jest podjęcie próby przeanalizowania polityki, jaką Turcja prowadzi wobec obcokrajowców poszukujących schronienia na jej terytorium. O ważkości zagadnienia zadecydowała w ostatnich latach przede wszystkim tocząca się w Syrii wojna domowa, w wyniku której na terytorium Turcji znalazło się ponad 700 tysięcy Syryjczyków. Szczególne w tym kontekście kontrowersje budzi fakt stosowania przez Turcję podwójnych standardów w przedmiocie nadawania imigrantom konwencyjnego statusu uchodźcy. Państwo to, jako jedno z czterech na świecie, w momencie przystępowania do Konwencji dotyczącej statusu uchodźców i Protokołu nowojorskiego zastrzegło sobie prawo do stosowania w tej materii tzw. kryterium geograficznego. W efekcie, o ile status uchodźcy nadany być może osobom przybywającym zza zachodnich granic Turcji, o tyle uciekinierzy z państw takich, jak Syria, Iran, czy Irak z formalnego punktu widzenia są „poszukującymi schronienia” (tur. sığınmacı). To zaś oznacza brak ich konwencyjnej ochrony. Celem artykułu jest jednak nie tylko przeanalizowanie prawnego i rzeczywistego położenia, w jakim znajdują się ofiary syryjskiej wojny domowej, przybywające na terytorium Turcji, a także próba przewidzenia scenariusza rozwoju tejże sytuacji. Celem uczynienia analizy możliwie najbardziej rzetelną, odwołano się zarówno do anglo, jak i tureckojęzycznych materiałów źródłowych.

Asynchronous Auction for Distributed Nonlinear Resource Allocation Problem

Resource Allocation Problems (RAPs) are concerned with the optimal allocation of resources to tasks. Problems in fields such as search theory, statistics, finance, economics, logistics, sensor & wireless networks fit this formulation. In literature, several centralized/synchronous algorithms have been proposed including recently proposed auction algorithm, RAP Auction. Here we present asynchronous implementation of RAP Auction for distributed RAPs.

On the Stable Paths Problem and a Restricted Variant

Interdomain routing on the Internet is performed using route preference policies specified independently, and arbitrarily by each Autonomous System in the network. These policies are used in the border gateway protocol (BGP) by each AS when selecting next-hop choices for routes to each destination. Conflicts between policies used by different ASs can lead to routing instabilities that, potentially, cannot be resolved no matter how long BGP is run. The Stable Paths Problem (SPP) is an abstract graph theoretic model of the problem of selecting nexthop routes for a destination. A stable solution to the problem is a set of next-hop choices, one for each AS, that is compatible with the policies of each AS. In a stable solution each AS has selected its best next-hop given that the next-hop choices of all neighbors are fixed. BGP can be viewed as a distributed algorithm for solving SPP. In this report we consider the stable paths problem, as well as a family of restricted variants of the stable paths problem, which we call F stable paths problems. We show that two very simple variants of the stable paths problem are also NP-complete. In addition we show that for networks with a DAG topology, there is an efficient centralized algorithm to solve the stable paths problem, and that BGP always efficiently converges to a stable solution on such networks.

Collocation Games and Their Application to Distributed Resource Management

We introduce Collocation Games as the basis of a general framework for modeling, analyzing, and facilitating the interactions between the various stakeholders in distributed systems in general, and in cloud computing environments in particular. Cloud computing enables fixed-capacity (processing, communication, and storage) resources to be offered by infrastructure providers as commodities for sale at a fixed cost in an open marketplace to independent, rational parties (players) interested in setting up their own applications over the Internet. Virtualization technologies enable the partitioning of such fixed-capacity resources so as to allow each player to dynamically acquire appropriate fractions of the resources for unencumbered use. In such a paradigm, the resource management problem reduces to that of partitioning the entire set of applications (players) into subsets, each of which is assigned to fixed-capacity cloud resources. If the infrastructure and the various applications are under a single administrative domain, this partitioning reduces to an optimization problem whose objective is to minimize the overall deployment cost. In a marketplace, in which the infrastructure provider is interested in maximizing its own profit, and in which each player is interested in minimizing its own cost, it should be evident that a global optimization is precisely the wrong framework. Rather, in this paper we use a game-theoretic framework in which the assignment of players to fixed-capacity resources is the outcome of a strategic "Collocation Game". Although we show that determining the existence of an equilibrium for collocation games in general is NP-hard, we present a number of simplified, practically-motivated variants of the collocation game for which we establish convergence to a Nash Equilibrium, and for which we derive convergence and price of anarchy bounds. In addition to these analytical results, we present an experimental evaluation of implementations of some of these variants for cloud infrastructures consisting of a collection of multidimensional resources of homogeneous or heterogeneous capacities. Experimental results using trace-driven simulations and synthetically generated datasets corroborate our analytical results and also illustrate how collocation games offer a feasible distributed resource management alternative for autonomic/self-organizing systems, in which the adoption of a global optimization approach (centralized or distributed) would be neither practical nor justifiable.

The Cache Inference Problem and its Application to Content and Request Routing

In many networked applications, independent caching agents cooperate by servicing each other's miss streams, without revealing the operational details of the caching mechanisms they employ. Inference of such details could be instrumental for many other processes. For example, it could be used for optimized forwarding (or routing) of one's own miss stream (or content) to available proxy caches, or for making cache-aware resource management decisions. In this paper, we introduce the Cache Inference Problem (CIP) as that of inferring the characteristics of a caching agent, given the miss stream of that agent. While CIP is insolvable in its most general form, there are special cases of practical importance in which it is, including when the request stream follows an Independent Reference Model (IRM) with generalized power-law (GPL) demand distribution. To that end, we design two basic "litmus" tests that are able to detect LFU and LRU replacement policies, the effective size of the cache and of the object universe, and the skewness of the GPL demand for objects. Using extensive experiments under synthetic as well as real traces, we show that our methods infer such characteristics accurately and quite efficiently, and that they remain robust even when the IRM/GPL assumptions do not hold, and even when the underlying replacement policies are not "pure" LFU or LRU. We exemplify the value of our inference framework by considering example applications.

Anisotropic Interpolation on Graphs: The Combinatorial Dirichlet Problem

The combinatorial Dirichlet problem is formulated, and an algorithm for solving it is presented. This provides an effective method for interpolating missing data on weighted graphs of arbitrary connectivity. Image processing examples are shown, and the relation to anistropic diffusion is discussed.

A Fuzzy ARTMAP Nonparametric Probability Estimator For Nonstationary Pattern Recognition Problem

An incremental, nonparametric probability estimation procedure using the fuzzy ARTMAP neural network is introduced. In slow-learning mode, fuzzy ARTMAP searches for patterns of data on which to build ever more accurate estimates. In max-nodes mode, the network initially learns a fixed number of categories, and weights are then adjusted gradually.

A Solution of the Figure-ground Problem for Biological Vision

A neural network model of 3-D visual perception and figure-ground separation by visual cortex is introduced. The theory provides a unified explanation of how a 2-D image may generate a 3-D percept; how figures pop-out from cluttered backgrounds; how spatially sparse disparity cues can generate continuous surface representations at different perceived depths; how representations of occluded regions can be completed and recognized without usually being seen; how occluded regions can sometimes be seen during percepts of transparency; how high spatial frequency parts of an image may appear closer than low spatial frequency parts; how sharp targets are detected better against a figure and blurred targets are detector better against a background; how low spatial frequency parts of an image may be fused while high spatial frequency parts are rivalrous; how sparse blue cones can generate vivid blue surface percepts; how 3-D neon color spreading, visual phantoms, and tissue contrast percepts are generated; how conjunctions of color-and-depth may rapidly pop-out during visual search. These explanations arise derived from an ecological analysis of how monocularly viewed parts of an image inherit the appropriate depth from contiguous binocularly viewed parts, as during DaVinci stereopsis. The model predicts the functional role and ordering of multiple interactions within and between the two parvocellular processing streams that join LGN to prestriate area V4. Interactions from cells representing larger scales and disparities to cells representing smaller scales and disparities are of particular importance.

Design Optimization and Security For Communication Networks

In this work we introduce a new mathematical tool for optimization of routes, topology design, and energy efficiency in wireless sensor networks. We introduce a vector field formulation that models communication in the network, and routing is performed in the direction of this vector field at every location of the network. The magnitude of the vector field at every location represents the density of amount of data that is being transited through that location. We define the total communication cost in the network as the integral of a quadratic form of the vector field over the network area. With the above formulation, we introduce a mathematical machinery based on partial differential equations very similar to the Maxwell's equations in electrostatic theory. We show that in order to minimize the cost, the routes should be found based on the solution of these partial differential equations. In our formulation, the sensors are sources of information, and they are similar to the positive charges in electrostatics, the destinations are sinks of information and they are similar to negative charges, and the network is similar to a non-homogeneous dielectric media with variable dielectric constant (or permittivity coefficient). In one of the applications of our mathematical model based on the vector fields, we offer a scheme for energy efficient routing. Our routing scheme is based on changing the permittivity coefficient to a higher value in the places of the network where nodes have high residual energy, and setting it to a low value in the places of the network where the nodes do not have much energy left. Our simulations show that our method gives a significant increase in the network life compared to the shortest path and weighted shortest path schemes. Our initial focus is on the case where there is only one destination in the network, and later we extend our approach to the case where there are multiple destinations in the network. In the case of having multiple destinations, we need to partition the network into several areas known as regions of attraction of the destinations. Each destination is responsible for collecting all messages being generated in its region of attraction. The complexity of the optimization problem in this case is how to define regions of attraction for the destinations and how much communication load to assign to each destination to optimize the performance of the network. We use our vector field model to solve the optimization problem for this case. We define a vector field, which is conservative, and hence it can be written as the gradient of a scalar field (also known as a potential field). Then we show that in the optimal assignment of the communication load of the network to the destinations, the value of that potential field should be equal at the locations of all the destinations. Another application of our vector field model is to find the optimal locations of the destinations in the network. We show that the vector field gives the gradient of the cost function with respect to the locations of the destinations. Based on this fact, we suggest an algorithm to be applied during the design phase of a network to relocate the destinations for reducing the communication cost function. The performance of our proposed schemes is confirmed by several examples and simulation experiments. In another part of this work we focus on the notions of responsiveness and conformance of TCP traffic in communication networks. We introduce the notion of responsiveness for TCP aggregates and define it as the degree to which a TCP aggregate reduces its sending rate to the network as a response to packet drops. We define metrics that describe the responsiveness of TCP aggregates, and suggest two methods for determining the values of these quantities. The first method is based on a test in which we drop a few packets from the aggregate intentionally and measure the resulting rate decrease of that aggregate. This kind of test is not robust to multiple simultaneous tests performed at different routers. We make the test robust to multiple simultaneous tests by using ideas from the CDMA approach to multiple access channels in communication theory. Based on this approach, we introduce tests of responsiveness for aggregates, and call it CDMA based Aggregate Perturbation Method (CAPM). We use CAPM to perform congestion control. A distinguishing feature of our congestion control scheme is that it maintains a degree of fairness among different aggregates. In the next step we modify CAPM to offer methods for estimating the proportion of an aggregate of TCP traffic that does not conform to protocol specifications, and hence may belong to a DDoS attack. Our methods work by intentionally perturbing the aggregate by dropping a very small number of packets from it and observing the response of the aggregate. We offer two methods for conformance testing. In the first method, we apply the perturbation tests to SYN packets being sent at the start of the TCP 3-way handshake, and we use the fact that the rate of ACK packets being exchanged in the handshake should follow the rate of perturbations. In the second method, we apply the perturbation tests to the TCP data packets and use the fact that the rate of retransmitted data packets should follow the rate of perturbations. In both methods, we use signature based perturbations, which means packet drops are performed with a rate given by a function of time. We use analogy of our problem with multiple access communication to find signatures. Specifically, we assign orthogonal CDMA based signatures to different routers in a distributed implementation of our methods. As a result of orthogonality, the performance does not degrade because of cross interference made by simultaneously testing routers. We have shown efficacy of our methods through mathematical analysis and extensive simulation experiments.